Here's a place where I can post my thoughts on new papers, provide updates on my projects, and post info that will eventually be on my website The Theropod Database - http://theropoddatabase.com/ . It will center on theropods, but may delve into other topics as well such as phylogenetics.

Sunday, January 31, 2010

Sereno (1999, 2001) presented 25 characters to support his versions of Ornithomimosauria (therizinosaurs, alvarezsaurs and ornithomimosaurs- characters 1-6, 16 and 17 below) and Ornithomimoidea (alvarezsaurs and ornithomimosaurs- characters 7-15 and 18-25). They are analysed below with special attention paid to their condition in Haplocheirus and Nqwebasaurus, the latter suggested to be part of this clade by Sereno. In addition, when a character is used by Choiniere et al. (2010), I've noted which avetheropods they miscoded and which they didn't code but could have. I term Sereno's hypothesis "arctometatarsalian alvarezsaurs" since by definition, all taxa closer to Ornithomimus than to birds are Arctometatarsalia.

1. Subnarial foramen absent. This is not in the TWG matrices, but is in Choiniere et al.'s. Miscoded- Sinraptor, Juravenator, Garudimimus, Gallimimus, Dromiceiomimus ("Ornithomimus"), Citipati. Not coded- Neovenator, Acrocanthosaurus, Dilong, Ornitholestes, Harpymimus, Struthiomimus, Sinovenator, Sinornithosaurus, Velociraptor. Haplocheirus has a subnarial foramen, so this would only be an ambiguous synapomorphy supporting arctometatarsalian alvarezsaurs.

2. Maxillary preantorbital ramus >50% length of antorbital fossa. Not in TWG or Choiniere et al.. This is untrue for Haplocheirus, but also for Shuvuuia and most ornithomimosaurs including the basal Pelecanimimus and Harpymimus. It does not support arctometatarsalian alvarezsaurs.

3. Antorbital fossa with invaginated ventral margin. This in the TWG matrices, but not Choiniere et al.'s. It seems to be untrue in Haplocheirus and Mononykus, so does not support arctometatarsalian alvarezsaurs.

4. Nasal anteroventral process absent. Not in TWG or Choiniere et al.. This is untrue for Haplocheirus, so this would only be an ambiguous synapomorphy supporting arctometatarsalian alvarezsaurs.

5. Internal mandibular fenestra reduced to a narrow slit or absent. This is in both the TWG and Choiniere et al. matrices. Unfortunately, it is basically repeated another time in Choiniere et al.'s matrix with their character "posterior end of splenial: straight (0); forked (1)", since the slit-like fenestra is primarily caused by the lack of posterior splenial concavity. Miscoded- Ornitholestes, Caudipteryx. Not coded- Acrocanthosaurus, Gorgosaurus ("Albertosaurus"), Garudimimus, Gallimimus, Struthiomimus, Segnosaurus, Chirostenotes, Conchoraptor, "Ingenia", Tsaagan, Shenzhouraptor ("Jeholornis"), Confuciusornis. Haplocheirus has this, potentially supporting arctometatarsalian alvarezsaurs.

Haplocheirus skull (modified from Choiniere et al., 2010) showing some character states which agree (green) and disagree (red) with placing alvarezsaurids in Arctometatarsalia.

8. Prefrontal dorsal exposure larger than lacrimal. Not in TWG or Choiniere et al.. It seems to be untrue in Haplocheirus and Harpymimus, so does not support arctometatarsalian alvarezsaurs.

9. Enlarged prefrontal orbital flange. Not in TWG or Choiniere et al.. It is moderately developed in Haplocheirus, potentially supporting arctometatarsalian alvarezsaurs.

10. Dentary at least 80% of mandibular length. Not in TWG or Choiniere et al.. It is absent in Haplocheirus, Shuvuuia and ornithomimosaurs, so does not support arctometatarsalian alvarezsaurs.

11. Maxillary and dentary teeth implanted in groove. In Choiniere et al. and in the TWG matrix since Makovicky et al. (2005). Choiniere et al. actually split the character into maxillary and dentary characters, as in their matrix troodontids have the latter but not the former. As the condition in Shuvuuia is only known for the dentary (Suzuki et al., 2002), only that character is discussed here. Miscoded- Caudipteryx, Unenlagia, Rahonavis, Utahraptor, Achillobator. Not coded- Neovenator, Carcharodontosaurus, Giganotosaurus, Falcarius, Beipiaosaurus, Shenzhouraptor. The coding of several taxa which lack teeth or preserved dentaries is disturbing. Also odd is that while derived oviraptorosaurs are rightly coded as inapplicable due to a lack of dentary teeth, toothless ornithomimosaurs and birds are not. The condition is unknown in Haplocheirus but lacking in Harpymimus and Shenzhousaurus, so only ambiguously supports arctometatarsalian alvarezsaurs.

12. Posterior maxillary teeth absent. Not in TWG or Choiniere et al.. This is untrue in Haplocheirus, so only ambiguously supports arctometatarsalian alvarezsaurs.

13. Tooth size in maxillary and dentary rows uniform. Not in TWG or Choiniere et al. to the extent Sereno meant it, though a more homodont state is part of other characters which distinguished therizinosaurs. In any case, Haplocheirus, Pelecanimimus and Shenzhousaurus lack it, so it does not support arctometatarsalian alvarezsaurs.

14. Dentary teeth smaller than maxillary teeth. Not in TWG or Choiniere et al.. This is true in Haplocheirus, but also in nearly all theropods, so is not diagnostic as stated.

15. Chevrons four to five times longer than respective neural spines. Not in TWG or Choiniere et al.. This is untrue in Haplocheirus, Shuvuuia and ornithomimosaurs, so does not support arctometatarsalian alvarezsaurs.

16. Metacarpal I at least 60% of metacarpal II length. This is in Choiniere et al.'s matrix in the form of metacarpal I being "half or less" or "subequal" to metacarpal II in length, which is quite a poorly formed set of states (e.g. 75% fits neither of them). Technically, they speak of the difference between metacarpals II and III because they follow Xu et al.'s (2009) homology of tetanurine digits, which is especially confusing. They themselves forget to do it in character 283 and their supplementary discussion. The TWG started with a decent set of states for this character- "Metacarpal I half the length of metacarpal II (0) or less than half the length of metacarpal II (1), or subequal in length to metacarpal II (2)." but then redefined it to force alvarezsaurids to be non-homologous with ornithomimosaurs- "Metacarpal I half or less than half the length of metacarpal II, and longer proximodistally than wide transversely (0) or subequal in length to metacarpal II (1) or very short and wider transversely than long proximodistally (2)." Miscoded- Allosaurus, Gorgosaurus, Tyrannosaurus, "Ingenia". Not coded- Dilong, Daspletosaurus, Chirostenotes, Avimimus, Oviraptor, Conchoraptor, Mei, Epidexipteryx, Scansoriopteryx ("Epidendrosaurus"). In any case, Haplocheirus lacks it (40%), so only ambiguously supports arctometatarsalian alvarezsaurs (Harpymimus' condition is considered a reversal based on Deinocheirus and Pelecanimimus). Nqwebasaurus also has this.

17. Metacarpo-phalangeal joint of digit I with about fifteen degrees of maximum extension. Not in TWG or Choiniere et al., though the latter do code for extensor pit depth on metacarpals, which is somewhat correlated with it. The condition in Haplocheirus is undescribed, and it remains a potential support for arctometatarsalian alvarezsaurs (again while absent in Harpymimus it is present in Deinocheirus and Pelecanimimus). Nqwebasaurus lacks this.

18. Metacarpals I-III with 60-70% of shafts in mutual contact. Not in TWG or Choiniere et al.. This seems true in Haplocheirus based on the skeletal reconstruction, though a more detailed figure would be helpful for confirmation. The basal condition in ornithomimosaurs is ambiguous, as Deinocheirus,Harpymimus and "Grusimimus" lack it, though Pelecanimimus has it. It thus provides only weakly ambiguous support for arctometatarsalian alvarezsaurs. Nqwebasaurus lacks it.

19. Metacarpal III over 75% of metacarpal II's transverse width. This is absent in the TWG matrix. It is basically present in Choiniere et al.'s matrix, though the dividing ratio is 70%. Miscoded- Huaxiagnathus, Mononykus, Microraptor. Not coded- Gorgosaurus, Daspletosaurus, Pelecanimimus, Harpymimus, Shenzhousaurus, Dromiceiomimus, Gallimimus, Struthiomimus, Chirostenotes, Oviraptor, "Ingenia", IGM 100/44, Sinornithoides, Sinornithosaurus, Velociraptor, Scansoriopteryx, Epidexipteryx, Archaeopteryx, Shenzhouraptor, Sapeornis, Confuciusornis, Yixianornis, Apsaravis. It is absent in Haplocheirus according to their coding, and also in Mononykus and Deinocheirus so does not support arctometatarsalian alvarezsaurs. Nqwebasaurus also lacks it.

Haplocheirus manus (modified from Choiniere et al. 2010) showing the short metacarpal I (labeled as mcII) and distally placed flexor tubercles, which disagree and agree respectively with placing alvarezsaurids in Arctometatarsalia.

20. Marked flexor depression on distal end of phalanx I-1. Not in TWG or Choiniere et al.. This is not determinable in Haplocheirus from the figures and it remains a potential support for arctometatarsalian alvarezsaurs. It is also present in Nqwebasaurus.

21. Paired flexor processes on manual phalanx I-1. Not in TWG or Choiniere et al.. This is not determinable in Haplocheirus from the figures and it remains a potential support for arctometatarsalian alvarezsaurs. It is also present in Nqwebasaurus.

22. Dorsolateral (not dorsomedial as stated by Sereno- Suzuki et al., 2002) tubercle on manual phalanx I-1. Not in TWG or Choiniere et al.. This is not determinable in Haplocheirus from the figures and is probably not a synapomorphy for alvarezsaurs and ornithomimosaurs since Deinocheirus and Patagonykus lack it.

23. Manual flexor tubercles placed distally. This is present in the TWG matrix, though the character is a composite that also includes manual ungual curvature and flexor tubercle size. A better version is present in Choiniere et al.'s analysis, though that also includes the state "reduced to pyramidal nubbins, as in Limusaurus", which should not be there. Instead, taxa like Limusaurus should be coded for the placement of their tubercles, regardless of size (which could be another character). Miscoded- Gorgosaurus, Shenzhousaurus, Haplocheirus, Epidexipteryx, Archaeopteryx. Not coded- Mapusaurus, Guanlong, Daspletosaurus, Ornitholestes, Troodon. From my measurement, Haplocheirus has the tubercle of manual ungual I placed 25% (at its highest point) down the length of the ventral curve, which is more distal than other taxa they coded as derived (e.g. Ornithomimus). This only ambiguously supports arctometatarsalian alvarezsaurs though, since Deinocheirus lacks it. Nqwebasaurus has it.

24. Ventral surface of manual unguals flat. Not in TWG or Choiniere et al.. This is not determinable in Haplocheirus from the figures, but is absent in Patagonykus and Albertonykus, so does not support arctometatarsalian alvarezsaurs.

25. Ilia nearly contact dorsally. This is not in the TWG matrix, but is in Choiniere et al.'s. Miscoded- Archaeornithomimus, Rahonavis. Not coded- Sinraptor, Stokesosaurus langhami, Gorgosaurus, Daspletosaurus, Shenzhousaurus, Gallimimus, Struthiomimus, Achillesaurus, Shuvuuia, Alxasaurus, Segnosaurus, Avimimus, Conchoraptor, "Ingenia", Microraptor, Scansoriopteryx, Epidexipteryx, Archaeopteryx, Sapeornis, Confuciusornis. It's particularly problematic that no alvarezsaurids were coded for this character, even ignoring the other omissions. This is not known in Haplocheirus and remains a potential synapomorphy of alvarezsaurs and ornithomimosaurs, though Alvarezsaurus' condition is controversial.

So of Sereno's 25 characters, only eight remain as potential synapomorphies. Another seven could support it under ACCTRAN, and the other ten are invalid. Choiniere et al.'s analysis only included three of the eight unambiguous characters, and four of the ambiguous ones. It was thus not a valid test of Sereno's hypothesis. It's good to note that just because 8-15 of these characters could support arctometatarsalian alvarezsaurs doesn't mean they necessarily would even if included in an analysis. For instance, Falcarius also has paired flexor processes on phalanx I-1, so maybe this character is primitive for Maniraptoriformes instead.
In addition to the flexor tubercle character above, several characters of Haplocheirus are miscoded based on the figures. Based on figure S5 with its only slightly concave posterior splenial edge, the internal mandibular fenestra is small and slit-like. The anterior dorsal diapophyses are long and extend far laterally past the zygapophyses, unlike derived alvarezsaurids and many maniraptorans. The coracoid has a deep notch below the glenoid, which is an ornithomimosaur character. The obturator process is placed proximally (~21% down the ischium) like ornithomimosaurs and more basal taxa (e.g. Gorgosaurus 28%, Tyrannosaurus 29%, Compsognathus 28%, Ornitholestes 27%, Archaeornithomimus 31%), not at midlength like that of maniraptorans. There is no distal notch between the obturator process and ischial shaft. The skeletal reconstruction shows a deep cleft between the anterior and greater trochanters, which is expected as Alvarezsaurus and Achillesaurus also show this condition (though they are also miscoded).

When these characters and those noted above are corrected in the matrix, the resulting cladogram is broadly similar to what the original matrix found (see below). Exceptions are that Stokesosaurus is sister to Dilong with Guanlong the most basal tyrannosauroid, alvarezsaurs and therizinosaurs are successively closer outgroups to Oviraptorosauria + Paraves, there is no resolution within Therizinosauroidea, Conchoraptor and "Ingenia" are sister taxa, Deinonychosauria and Dromaeosauridae exist with normal content, Rahonavis and Archaeopteryx are basal avialans, and Shenzhouraptor is sister to Confuciusornis, with that pair sister to scansoriopterygids. It only takes three more steps to make alvarezsaurs and ornithomimosaurs are sister taxa, and Ornitholestes and Compsognathidae form successively further outgroups to Maniraptoriformes. You might be thinking the changes made arctometatarsalian alvarezsaurs less likely, since Choiniere et al. reported only one more step was necessary. However, from what I can tell, Choiniere et al. never found the most parsimonious trees in their dataset. Running it in PAUP with the same characters ordered results in trees 1887 steps long, not 1998 steps as reported by the authors. I think the problem is that they used TNT, which has resulted in few and suboptimal trees for me in the past. With Choiniere et al.'s original codings for the characters noted above, it takes five more steps to force arctometatarsalian alvarezsaurids. So really, changing the codings improved their liklihood by two steps. The actual most parsimonious consensus tree from their data is (compare to their figure S1)-

Thursday, January 28, 2010

While I prepare an official blog post on Haplocheirus (skeletal above from Choiniere et al., 2010), the new basal alvarezsaur, there are a couple comments I want to make. The abstract states it "confirms that this group is a basal member of Maniraptora, the clade containing birds and their closest theropod relatives," but their matrix finds alvarezsaurs sister to ornithomimosaurs with the addition of ONE extra step. One measley step finds Sereno's hypothesis to be supported. That's not confirmation of anything. That's basically ambiguous. In fact, excluding Haplocheirus from the analysis actually results in trees where alvarezsaurs are not placed as basally as they are in some of the trees from the full analysis, so it makes the clade more basally placed if anything. But wait, in the supplementary info they REDEFINE Maniraptora. Now all of a sudden, Maniraptora is "Ornitholestes, Archaeopteryx, their most common recent ancestor and all of its descendants." I know Phylocode isn't official yet, but why change a definition after over a decade of stability and consistancy? Everyone agrees alvarezsaurs are maniraptorans under that definition (just check out Sereno's trees and my website's phylogeny). Hell, ornithomimosaurs are (otherwise impossibly) maniraptorans under that definition in my tree. In any case, I'm adding Haplocheirus to my coelurosaur supermatrix along with all of the supposed arctometatarsalian and bird characters of alvarezsaurids and we'll see what that says today or Friday. Maybe they'll be unambiguously maniraptoran, but it won't be because I change the definition of the latter clade.

Monday, January 25, 2010

Here's a change in pace for a blog entry. Instead of examining a taxon, I'll examine an analysis. In the spirit of the new NMMNH volume about drepanosaurids, let's examine the closest thing to a theropod-drepanosaurid cross. Way back in 1991, Chatterjee published his first Protoavis monograph which described the skull. He included a cladistic analysis that placed Protoavis closer to modern birds than Archaeopteryx, in what I would call Ornithurae (sensu Gauthier 1986, not to be confused with the more restrictive Ornithurae versions Chiappe or Clarke use; ahhh taxonomy....). So I decided to look through Chatterjee's characters and codings to determine their quality. Of course we know Protoavis is a chimaera now, but the skull was considered most intriguing by Witmer (2001) and no cranial elements have been shown to be misidentified or non-theropodan yet. So by accepting Chatterjee's identifications for the skull at least we're not definitely miscoding things like we would be if we coded the "metacarpus" or something. At the end I even add Megalancosaurus to the matrix to see what that does. A warning- most of this post consists of criticisms of specific characters which are easy to get bogged down in, bringing it to downright TetZooesque proportions. So for the fun part, you might want to skip to the General analysis conclusions. I'm sure at least David Marjanovic will appreciate it. ;) But without further ado, Chatterjee's phylogeny using his nomenclature-

Theropods- This is of course paraphyletic to the ingroup. Chatterjee mentions several theropods in his comparison of Protoavis to that group- Megapnosaurus, Dilophosaurus, Allosaurus, Tyrannosaurus, Ornithomimidae, Troodon and Dromaeosaurus. These will be used for coding.

1. This character (metotic structure) deserves comment. Chatterjee identifies a "metotic ossification" in Protoavis which spans the area between the paroccipital process and basal tubera, separating the fenestra pseudorotunda from the vagus (X) nerve. This structure is seemingly part of the exoccipital-opsthotic (there is no suture) and causes the vagus nerve to exit on the occipital surface. This is the same as what's usually called the metotic strut in theropods, but Chatterjee codes theropods as lacking the character. The text makes it clear that he believes the theropod structure (which he terms a subcapsular process) is non-homologous with the avian structure because Rieppel (1985) found that the subcapsular process in crocodilians develops from the exoccipital while the metotic strut of birds arises from a separate condensation. Yet developmental processes also evolve, and the condition in theropod development is unknown in any case. Even worse, the developmental origin of the structure in Protoavis, Archaeopteryx or Hesperornis is also unknown, making Chatterjee's coding for them as having a metotic and not a subcapsular process an a priori assumption based on his "knowing" they are birds. As derived theropods (e.g. Dilophosaurus- Welles, 1984; Tyrannosaurus- Brochu, 2003; Troodon- Currie and Zhao, 1994; Dromaeosaurus- Currie, 1995) have a metotic strut identical to the condition in Protoavis and Archaeopteryx, theropods are coded as polymorphic. Avimimus (Kurzanov, 1986) and Ichthyornis (Clarke, 2004) also have metotic struts. The condition in Protoavis is illustrated by Chatterjee as having a metotic strut, but comparing it to "Megapnosaurus" kayentakatae suggests it's possible the supposed anterior opening of the posterior tympanic recess is the actual vagus nerve, while the supposed vagus foramen could be the larger of two hypoglossal (XII) foramina. Witmer (2001) had no problem with the metotic strut interpretation however. In any case, Protoavis is coded unknown pending further study.

Top row- Protoavis braincase after Chatterjee (1991) in posterior and left lateral view; "Megapnosaurus" braincase in posterior view after Tykoski (1998).

2. This character is the unquantified "small olfactory lobes", which is coded as present in all bird taxa and absent in the outgroups. Comparing olfactory bulb width to cerebrum width does indeed suggest Archaeopteryx has narrower bulbs (27%) than Troodon (32%) or Dromaeosaurus (48%). However, Avimimus is described as having "relatively large" olfactory bulbs by Kurzanov (1985) and the skull seems broken posterior to where the bulbs were placed anyway, with the small triangular olfactory (I) nerve foramen visible in anterior view. Avimimus is thus recoded as unknown. Edinger (1951) indicates that Marsh's (1888) endocast of Hesperornis was largely imaginary and notes no data concerning olfactory bulb size can be determined from the specimens. Whether newer specimen KUVP 71012 can shed light on its morphology is unknown, as this area has not been described. Hesperornis is recoded unknown. While no ventral illustration of the frontals or dorsal/ventral illustration of Protoavis' endocast is shown, the drawing of the brain (figure 16d) by Chatterjee indicates its olfactory bulbs were ~42% as wide as the cerebra. So assuming the composite endocast is even trustworthy, Protoavis would seem to have large olfactory bulbs. It is here provisionally coded as unknown.

3. Character 3 is cerebellar fossa extended on to supraoccipital, but contra Chatterjee this is seen in even basal theropods (e.g. Ceratosaurus- Sanders and Smith, 2005; Tyrannosaurus- Osborn, 1913). The Ichthyornis material is far too crushed to determine this character's presence.

4. This character involves the presence of a cerebral vein ("sinus canal") penetrating the supraoccipital-epiotic suture. This is present in theropods as well ('caudal middle cerebral vein' of "Megapnosaurus" katentakatae in Tykoski, 1998; 'dorsal cerebral vein' of Tyrannosaurus in Brochu, 2003; 'posterior canal of the middle cerebral vein' of Dromaeosaurus in Currie, 1995).

5. Troodon lacks a prefrontal (Russell, 1969), making theropods polymorphic. The condition in Gobipteryx is uncertain, as no specimen preserves that area. The presence of this bone is uncertain in Protoavis, as the lacrimal is preserved attached to the maxilla, while the frontal is not just preserved separately, but comes from a different larger individual. Thus they cannot be articulated, and the frontal itself only seems to bear an anterior (nasal?) articular surface, with no apparent lateral articular surface for a lacrimal and/or prefrontal.

6. Chatterjee's next character is confusing. It is "braincase: (basioccipital-basisphenoid-parasphenoid complex): (0) vertical; (1) horizontal." Chatterjee elaborates by discussing the outgroups' braincase as deep, but birds' as flat. Yet the braincase of Archaeopteryx does not differ much from Troodon's in overall proportions. The ventral braincase of most small theropods (Megapnosaurus, Troodon, etc.) is basically horizontal, with an anteriorly directed parasphenoid cultriform process. Most theropods' ventral braincase is deeper than birds' due to a vertically deep basisphenoid sinus, and even taxa like Troodon which lack an external sinus have deep internal sinuses there. Unfortunately, sinus depth is difficult to measure in most specimens, though coelophysids have shallower sinuses than other theropods (Raath, 1989). Protoavis has a sinus on the ventral surface of its supposed basioccipital, though the depth of the element is never illustrated. It would resemble coelophysids if not for the supposed basisphenoid (Witmer, 2001 doubted its identity) from a different individual with its small basipterygoid processes. The reason for coding Archaeopteryx as derived is uncertain, as the Munich specimen is the only one which preserves this area and was not known until after Chatterjee's paper was published. In any case, its deep basipterygoid processes suggest a deep sinus if anything (Elzanoski and Wellnhofer, 1996). Avimimus and Ichthyornis are also unknown, as their articulated braincases do not allow ventral depth to be measured. Dibothrosuchus has a deep basisphenoid like theropods, though due to the ventrally projecting basipterygoid processes, as it lacks a ventral basisphenoid sinus. The question remains how to code this character. The condition in most theropods is non-homologous with sphenosuchids, Protoavis may resemble coelophysids, and Hesperornis has a flat morphology due to lacking promiment basipterygoid processes or a ventral sinus. It is here deleted (so all eight taxa are recoded as unknown), though basiphenoid sinus depth or basipterygoid process size might be good substitutes.

7. This character involves the external naris being posteriorly placed, and indeed Archaeopteryx, Gobipteryx and Hesperornis have more posteriorly placed nares than the included avetheropods (distance from snout tip to front of nares 20% or more of height of orbit+jugal). But Megapnosaurus and Dilophosaurus have nares placed more posteriorly than Archaeopteryx, making theropods polymorphic. The condition in Ichthyornis is unknown as the described premaxillary fragment does not indicate the nares' anterior edge. Protoavis actually has a rostrally placed naris based on the illustrated premaxilla and posterior skull of the large individual, though Chatterjee changed this for his cranial reconstruction to more closely resemble birds.

8. Archaeopteryx has a complete postorbital, which probably contacted the jugal (Tischlinger, 2005). The condition in Gobipteryx is unpreserved. Protoavis is supposed to lack a postorbital based on a lack of facets on the frontal and squamosal, which were confirmed by Witmer (2001). Yet the laterosphenoid has a large capitate process (termed the postorbital process by Chatterjee) with what appears to be an articular surface, which fits into a socket on the postorbital in most theropods. The jugal is described as having only a rudimentary dorsal process, though the original material is only illustrated in ventral view. Thus there is not a complete lack of postorbital articular surfaces, and the evidence is contradictory. Perhaps being such a small or juvenile individual, Protoavis did not have a strongly attached postorbital. For now, it is tentatively coded as unknown.

9. This character (maxillary tooth row ends anterior to antorbital fenestra) is coded as an autapomorphy of Archaeopteryx, making it useless for the analysis and artificially increasing the CI. However, Archaeopteryx actually lacks this character as shown by the Eichstatt specimen (Paul, 2002). Even worse, Protoavis and Gobipteryx are coded as lacking it, despite not having maxillary dentition at all! Similarly, even if the premaxillary denticles of Avimimus are interpreted as teeth (contra Vickers-Rich et al., 2002), the maxilla is unpreserved. Ichthyornis only preserves a small maxillary fragment of uncertain position (Clarke, 2004). All of these taxa should be coded as unknown. The condition in Hesperornis is difficult to code, as a medial antorbital wall which defines the antorbiral fenestra anteriorly in more basal theropods is generally thought to be absent (Witmer, 1990). Even if the palatine process is homologous, without it extending dorsally, there is no way to judge an anterior boundary to the antorbital fenestra. Hesperornis is thus recoded as unknown.

10. The fused quadratojugal and quadrate in Avimimus make judging the presence of a dorsal quadratojugal process impossible. Neither Gobipteryx or Ichthyornis preserve the quadratojugal, so are both recoded as unknown. The quadratojugal of Protoavis is posterodorsally curved in the material, unlike Chatterjee's reconstruction. This posterodorsal section would seem to be a valid dorsal process, so Protoavis is recoded.

Top- Protoavis posteroventral skull as preserved. Bottom- Same area as reconstructed by Chatterjee. Both drawn to same jugal length, quadratojugal colored orange. Note also how much more robust and unbirdlike the jugal is in the actual material. Both after Chatterjee (1991).

11. This character (premaxillary teeth present but anterior dentary teeth absent) is another supposed autapomorphy, and is problematic for being a composite as well. It combines a primitive state for one element (premaxillary teeth present) with a derived one from another element (anterior dentary teeth absent). The latter is also present in some theropods (e.g. ornithomimids) and Gobipteryx, so those are changed to polymorphic and derived respectively. The condition in Protoavis is uncertain, as the one anterior dentary fragment seems broken at both ends, making its position unknown.

12. This character (temporal configuration fully modified) is correlated with character 8 (diapsid temporal configuration partially modified). Thus all taxa coded 0 for character 8 (sphenosuchids, theropods, Archaeopteryx) are coded unknown. Gobipteryx and Protoavis are again coded as unknown.

13. Chatterjee's 13th character is "alaparasphenoid covers anterior tympanic recess." The alaparasphenoid of birds is homologous to the structure variously called the crista prootica, otosphenoidal crest, ala basisphenoid and preotic pendent in theropods. In some theropods (e.g. Allosaurus- Chure, 2000; Tyrannosaurus- Brochu, 2003), this covers the anterior tympanic recess. Theropods are thus recoded as polymorphic. Archaeopteryx has only a small ridge, so is coded as plesiomorphic. While the supposed alaparasphenoid of Protoavis (on the possible basisphenoid) does not seem to have much projection posterodorsally to cover the anterior tympanic recess, the prootic fragment has a dorsal overhang (figure 12f) that is similar to that in Megapnosaurus.

14. Chatterjee codes the zygomatic process of the squamosal as lacking in theropods, but it is homologous to the quadratojugal process, which is present in almost all theropods. Theropods are recoded as having the process. Fusion makes its presence in Avimimus uncertain (Kurzanov, 1987), while Archaeopteryx has the process (Elzanowski and Wellnhofer, 1996). The squamosal of Gobipteryx is unknown. The squamosal of Protoavis is described as having a zygomatic process, but this is clearly the anterior process instead, as it is the one Chatterjee notes is peculiar in lacking a postorbital facet. Thus assuming it is complete, Protoavis actually lacks a significant ventral process.

15. Witmer (2001) notes the supposed quadratojugal cotyla of Protoavis' quadrate is subtle and "not all that different" from other theropods such as Deinonychus or juvenile tyrannosaurids. It is thus recoded as absent. The condition in Avimimus is uncertain, as the quadratojugal is fused to the quadrate. The area of contact is unpreserved in Gobipteryx's quadrate (Elzanowski, 1977).

16. This character (orbital process of quadrate present) involves the pterygoid's articulation with the quadrate more than the quadrate's structure itself, as sphenosuchians and theropods both have the homolog to an orbital process (the pterygoid process). Yet in derived birds, the pterygoid only articulates with the quadrate ventrally, leaving the former pterygoid process free. The condition in Protoavis is difficult to determine, as Witmer (2001) noted the supposed pterygoid condyle of the quadrate was not present. The pterygoid's quadrate ramus is described as a narrow bar though, which would indeed have trouble articulating in a broad overlapping suture typical of theropods. Protoavis' derived coding is tentatively retained.

17. This character (pterygoid condyle present on quadrate) is correlated with the previous one, as only a taxon with a free orbital process will have a pterygoid condyle. Thus sphenosuchids, theropods, Archaeopteryx and Avimimus are all recoded as unknown. As noted above, the pterygoid condyle on Protoavis' quadrate is not there according to Witmer (2001), so Protoavis is changed to plesiomorphic.

18. Gobipteryx (Chiappe et al., 2001) and Hesperornis (Witmer, 1990) have large dorsal maxillary processes, so are recoded. That of Protoavis was originally illustrated as broken off (although described as absent), but Chatterjee (1999) later described a new element as the maxilla, this time with a large dorsal process (illustrated in Chatterjee, 1998). Assuming this is really a maxilla, it does indeed have a large process. Protoavis is recoded.

19. This character involves cranial kinesis, which is especially difficult to demonstrate in fossils (Holliday and Witmer, 2008). Specifically, it involves prokinesis, which needs several components to function- mobile joints at the nasofrontal, quadrato-otic, quadrato-quadratojugal, maxillojugal and anterior palate, and loss of a connecting postorbital, epipterygoid and ectopterygoid. Based on their criteria, Gobipteryx probably lacked prokinesis due to its ectopterygoid so would need to be recoded. The condition in Protoavis is complicated by incompleteness and uncertain identification. The nasofrontal joint does indeed seem to be reduced, and like most theropods the quadrate has a synovial joint with the sqmousal. While perhaps not a true ball and socket joint, the quadrate-quadratojugal articulation is loose and convexoconcave. However, the maxilla appears to have a broad, forked articulation with the jugal. The evidence it lacked a postorbital is ambiguous (see above), and the absence of small elements such as epipterygoids and ectopterygoids even more so. Note this character is correlated with characters 8, 10, 12, 15, 16 and 20, so is deleted and all seven taxa recoded unknown.

20. The ectopterygoid is present in Gobipteryx (Elzanowski, 1995), while its absence in Protoavis cannot be demonstrated given the disarticulation of the material.

21. Clarke (2004) notes both Hesperornis and Ichthyornis have a bicondylar quadrate, with the supposed caudal condyle being a posterior continuation of a single medial condylar surface. The tricondylar quadrate of Protoavis is supposedly illustrated in figure 11 of Chatterjee's 1991 paper, but that figure is actually missing. Still, the paratype quadrate is illustrated in his 1998 paper as being tricondylar, so is provisionally still coded that way. Witmer (2001) notes the holotype's quadrate seems to lack mandibular condyles at all.

22. Like character 11, this is both a useless autapomorphy, and also a composite character. Supposedly an apomorphy of Protoavis, it is "teeth restricted to tips of premaxilla and dentary." The two illustrated premaxillary alveoli are in the middle of the bone, while Chatterjee describes a total of three alveoli which are "in front." Chatterjee claims there were only two anteriorly placed dentary teeth, but the only section of dentary preserved which would be expected to have teeth is from an unknown position and is associated with three disarticulated teeth (one supposedly a replacement tooth). Assuming it is even a dentary and the teeth belong to that bone, there is no way of knowing how they were distributed. The potentially toothless posterior portion of the premaxilla is matched by some theropods such as coelophysoids, while Avimimus, Gobipteryx, Hesperornis and Ichthyornis lack premaxillary teeth entirely. Thus Protoavis is tentatively coded as lacking posterior premaxillary teeth, theropods are coded as polymorphic, and Gobipteryx, Hesperornis and Ichthyornis are coded as apomorphic (Avimimus' posterior premaxillae are unpreserved).

23. The nasals do not contact on the median in Ichthyornis (Clarke, 2004).

24. This character (nasal process of premaxillae extend posteriorly to lacrimals) is directly correlated with the previous one (nasals do not contact on median), as the premaxillae are what separates the nasals from one another. It is therefore deleted and the eight coded taxa recoded as unknown.

25. The mesethmoid is ossified in many theropods (e.g. Tyrannosaurus- Hurum and Sabath, 2003; Troodon- Ali et al., 2008; Dromaeosaurus- Currie, 1995), so Theropoda is recoded as polymorphic. Avimimus also has this element (Kurzanov, 1981), as does Ichthyornis (Clarke, 2004). Its presence in Archaeopteryx and Protoavis is uncertain due to the lack of articulated material in the latter and easy separation from the laterosphenoids and frontals.

26. This is another useless autapomorphy, and yet again the taxon in question (Hesperornis) does not exhibit the feature (pterygoid process fits into basisphenoid facet), as Hesperornis has low but convex basipterygoid processes (Elzanowski, 1991). The condition in Avimimus is uncertain due to fusion (Kurzanov, 1987), while the condition in Ichthyornis is uncertain as the basipterygoid area is unpreserved (Clarke, 2004).

27. Another autapomorphy that Hesperornis does not in fact possess, and a composite character to boot- "combination of short, complex pterygoid with narrow, elongate palatine." Chatterjee misidentifies the palatal elements of Hesperornis (Chatterjee, 1991), which only appears to have a short pterygoid because of the unfused anterior portion (hemipterygoid of Elzanowski). The real palatine of Hesperornis is indeed narrow and elongate, but those of Avimimus, Gobipteryx and Ichthyornis are unpreserved. The palate of Protoavis is very difficult to intrepret, but the supposed choana makes more sense as a suborbital fenestra given its position behind the maxillojugal suture. Any coding regarding the shape of its palatines should be changed to unknown.

28. This character (pterygoid condyle of quadrate large) is correlated with character 17 (pterygoid condyle present), so any taxa scored as 0 for 17 (sphenosuchids, theropods, Protoavis, Avimimus, Archaeopteryx) should be coded unknown for this one. However, the character is still a useless autapomorphy, being found only in Ichthyornis.

29. This character (toothless jaws) is correlated with parts of 11 (dentary teeth absent) and 22 (posterior premaxillary teeth, maxillary teeth, and posterior dentary teeth absent). It is intended as an apomorphy of Gobipteryx, making it useless. However, as Gobipteryx differs from most included taxa by lacking maxillary teeth specifically, that portion of the character is retained for this analysis. Protoavis apparently also lacks maxillary teeth, so is recoded. Some theropods (e.g. ornithomimids) lack them as well, and Avimimus does not preserve the maxilla.

30. The final character is another useless apomorphy of Gobipteryx- dentary symphysis fused. Protoavis cannot be scored for it, as the anteriormost dentary portion is unpreserved.

General analysis conclusions- This is a highly flawed analysis. It only uses characters from one area of the body, which makes it less reliable. Also, it only uses characters which are known in Protoavis, a trend which is common when authors are trying to phylogenetically place their taxon under study. Yet characters unpreserved in Protoavis could nonetheless strongly support the topology of the tree, which will in turn affect character distribution and thus Protoavis' placement. The characters are all designed to support certain clades, so this is another cladistic demonstration instead of a cladistic analysis. Having an all-zero outgroup is generally flawed, and in this case theropods should be scored as 0/1 or for 11 (37%) of the characters, though sphenosuchids do indeed seem to be coded correctly as all zero. Nine of the characters (30%!) are designed to be autapomorphies, which do not influence the analysis at all, making the already small matrix even smaller. 6 (20%) of the characters are correlated with other characters. Characters 11, 22 and 27 are especially poorly formed, as they involve the morphology of more than one element each. Several times Chatterjee assumes non-homology between avian and theropod features (metotic strut, alaparasphenoid, zygomatic process) and codes as if this assumption were necessarily true. Taxa are commonly coded for elements they do not preserve (especially Ichthyornis and Gobipteryx) or for characters which are inapplicable (tooth characters in toothless taxa, articulation characters in taxa with fusion). In total, 110/240 (46%) of the characters are miscoded. When recoded, the new result (with my terminology) is-

The resolution is decreased, which isn't surprising since there are only 11 parsimony-informative characters left.

Neither the original or recoded analysis provides much support at all for placing Avimimus closer to modern birds than Archaeopteryx, as it moves to a more traditional placement with only one more step. The original analysis did provide moderate support for placing Protoavis in this position (9 steps), but once recoded its position relative to Archaeopteryx is basically ambiguous (1 step). Sauriurae was rejected with moderate confidence originally (10 steps), but recoding has made this support weak (3 steps). Basically, Chatterjee's matrix is too small to securely reject any plausible hypothesis.

Experiments with controversial taxa- It's somewhat pointless to add more taxa to a matrix with such little power to resolve relationships. One question might be if resolution is improved by deleting the chimaerical Protoavis. Another is if more basal oviraptorosaur such as Incisivosaurus would cause Avimimus to be excluded from birds. If Protoavis includes some drepanosaurid elements, adding Megalancosaurus to the matrix might be informative. Finally, it is odd that Chatterjee excluded modern Aves. Deleting Protoavis has no effect on tree topology or resolution. Megalancosaurus, Incisivosaurus and Aves were all added as OTUs. The resulting tree is-

Avimimus still falls out as a bird, though Gobipteryx has a more stable position more derived than Protoavis. The fact Megalancosaurus falls out by Protoavis within Theropoda is yet more indication this matrix is insufficient to test phylogenies. Megalancosaurus is excluded from Theropoda with 1 more step.

Wow! Support for Megalancosaurus as a bird! Feduccia was right all along. ;) Or rather, a near ambiguous result in a small matrix. This is a good example of why small matrices should not be trusted, and why when a taxon's position is only supported by one extra step, it's as likely as not that the cladogram is wrong.

Chatterjee, 1991. Cranial anatomy and relationships of a new Triassic bird from Texas. Philosophical Transactions of the Royal Society of London Series B. 332(1265), 277-342.

Saturday, January 23, 2010

Thanks to everyone for their comments! Don't expect daily posts to be the norm, but I've been studying "Poekilopleuron" schmidti, so on to post number two. This is another obscure Russian theropod described briefly and thrown into Megalosauridae or Theropoda indet. ever since. It has the additional notoriety of having its main element reidentified 90 years after it was described, but looking at the figures, I don't think either identification is correct.

Here's a figure I made showing "Poekilopleuron" schmidti compared to some elements from other dinosaurs (click to be able to read it). Compare yourself and see if you come to the same conclusions I did. "Poekilopleuron" schmidti's figures are taken from Kiprijanow (1883), Mapusaurus' from Coria and Currie (2006), Chilantaisaurus' from Benson and Xu (2008), Amurosaurus' from Godefroit et al. (2004), Ouranosaurus' from Taquet (1976), Epachthosaurus' from Martinez et al. (2004), the other titanosaurs' from Apesteguia (2005), Poekilopleuron bucklandii's from Allain and Chure (2002), Eustreptospondylus' from Sadlier et al. (2008), Megalosaurus' from Benson (2009), Barosaurus' from McIntosh (2005), Sinraptor's from Currie and Zhao (1994) and Tyrannosaurus' from Brochu (2003).

Previous diagnoses- Kiprijanow (1883) did not provide a formal diagnosis, but differentiated P. schmidti from P. bucklandii based on its later age and geographic separation. While the former near certainly means it is not conspecific, stratigraphy and biogeography are not currently viewed as valid criteria for erecting a new species.

Comments- Kiprijanow (1883) described Poekilopleuron schmidti based on a diapophysis and four small shaft fragments from the axial skeleton. He referred it to the Seweri Osteolith, which was recognized as being of Gault age (Albian). Molnar (1990) noted its age was difficult to determine, but stated it appeared to be Cenomanian-Santonian. Nessov (1995) believed it was Albian-Cenomanian instead based on his study of the area and also noted Neogene mammal fossils were present. While no catalogue numbers or repository were given by Kiprijanow, Storrs et al. (2000) stated his material is presumably in the Russian Academy of Sciences in St. Petersburg.

The diapophysis is large, about 132 mm wide at its end. The shaft is cylindrical and apparently hollow, with a bone wall to diameter ratio of ~23%. The end is asymmetrically expanded primarily in one plane, with one corner projecting to the side and end significantly more than the other. The less projected corner has the broken base of a large bump on one side, and a lower but more proximodistally elongate bump on the other side, the latter bump placed closer to the midline. Though saddle-shaped in one view, the distal surface appears irregularly bumpy in another, and no obvious condyles exist. The end's outline is roughly shaped like a flattened parallelogram, with one of the short sides being about twice as long as its opposite.

There are four small shaft fragments illustrated (table IV, figures 1-3). All are slightly curved with one end (proximal?) gently expanded, and broken both proximally and distally (minimum shaft width ~20-26 mm). It is difficult to tell which proximal edges are broken and which are natural. The element in figure 1 has a longitudinal ridge down the center of one side with fossae (perhaps caused by crushing) on either side of it at the proximal end. The proximal cross section (figure 1C) is very flat except for the ridge. The element in figure 3 is flat on both sides and has a triangular cross section distally (figure 3C'). Figure 2 seemingly consists of two elements judging by their different lengths, with 2A having a rounded surface and 2B having a longitudinally ridged surface.

Kiprijanow referred this material to Poekilopleuron (then thought to be a crocodile) because he thought the form of the elements was identical. However this is obviously not so as even if there is a general resemblence to Poekilopleuron's distal humerus in anterior view, side view shows at the very least schmidti lacks Poekilopleuron's deltopectoral crest. Further differences from theropod humeri are mentioned below. Rozhdestvensky (1973) reidentified the diapophysis as a distal tibia, referring it to Megalosaurus sp. (he included Poekilopleuron in that genus as well). This may be the origin of Olshevsky's (1991) combination Megalosaurus schmidti (listed as a junior synonym of P. schmidti), as it is not possible to sink a named species into "sp.", regardless of how undiagnostic it is. It would be quite coincidental if schmidti were still referrable to the same kind of animal, after the one somewhat diagnostic fragment's position was reinterpreted. Yet schmidti differs from both Poekilopleuron and Megalosaurus in lacking a shelf for the astragalar ascending process and sharply tapered lateral edge in distal view. Efimov and Chkhikvadze (1987) in a review of Soviet crocodilians, believed schmidti to be dinosaurian. Molnar stated it "could belong to almost any large Late Cretaceous theropod" and referred it to Theropoda indet., but no known theropod has a similar distal tibia, leading me to doubt its identity (see below). Molnar later (pers. comm. to Olshevsky, 1991) stated it may be ceratosaurid, but Ceratosaurus differs in the same major ways as Megalosaurus and Poekilopleuron. Nessov was doubtful of its theropod identity, based on a "slit-like pit" on the more broken side, "separating the region of contact with other bones from the side of the diaphysis." I'm unsure which feature Nessov was referring to, though the bone does have many cracks and small pits, the latter largely from wear showing the internal texture. Nessov thought the rib fragments were not obviously dinosaurian and probably belonged to marine reptiles (he discovered ichthyosaur remains at the site). Holtz et al. (2004) listed it as Tetanurae indet. without comment. Poekilopleuron schmidti is generally listed as Theropoda indet. in modern references.

The diapophysis was identified by Kiprijanow as a distal humerus and Rozhdestvensky as a distal tibia. However, it differs from both of these elements. Dinosaurian humeri have more symmetrical distal outlines as opposed to schmidti's one side being much deeper. Both condyles in theropods are usually projected anteriorly and rounded in side view, whereas schmidti has a prominent and elongate projection on only one side and tapers towards the end in side view. Most non-coelurosaur theropod tibiae have a deep shelf projecting diagonally across the anterior end for reception of the astragalar ascending process, which is lacking in schmidti. Coelurosaurs and a few other taxa lack this shelf, but always have a much shallower distal end which is strongly tapered on one side. This distal outline is even true of basal taxa like ceratosaurs and megalosauroids (though not the much earlier coelophysoids, which differ more strongly in having even deeper astragalar shelves), while coelurosaurs exaggerate it further. Another point of difference is that theropod tibial shafts are wider compared to the width of their distal transverse flare. Other dinosaur tibiae differ as well, with ornithopods having a very strongly projected lateral flange for instance. While schmidti bears a general resemblence to a proximal tibia, it lacks all the detailed features one would expect- posterior intercondylar groove, fibular crest, lateral condyle. Similarly, proximal fibulae are narrower, and ulnae more triangular in proximal view. An exhaustive comparison of dinosaur limb elements indicates it is near certainly a metapodial. The closest resemblence among theropods is to the proximal end of metatarsal IV of large carnosaurs such as Mapusaurus (mislabeled II in its description) and Chilantaisaurus. The primary differences are schmidti would have a flat anterior edge and a narrower shaft. Another similar element is metatarsal III in hadrosauriforms, but these differ in being broader proximally and having a more pronounced anteroproximal projection. More importantly, the anterior surface would be oddly angled in schmidti and it lacks the anteroposterior expansion distally which is a consequence of hadrosauriforms' short metatarsi. This makes it an unlikely identification. The most similar element I could find among dinosaurs is the proximal end of metacarpal IV of titanosauriforms. cf. Laplatasaurus' metacarpal IV is nearly identical in proximal view, while Epachthosaurus' is a close match in lateral view. The size is also well within the range of titanosauriforms, while only giant theropods are of comparable size. One point of contention is that schmidti's element is illustrated and described as being hollow, but it's possible this is taphonomic as the end is broken and extensively fractured, perhaps leading to the loss of a spongy interior as often happens in recent mammal bones. Unfortunately, if we accept the sauropod identification there is a high degree of variation ontogenetically/intraspecifically, so the element is Titanosauriformes indet.. Most other sauropods had stouter metacarpals and were extinct by the Mid Cretaceous in any case.

Kiprijanow identified the shaft fragments as ribs without specifying which part of the vertebral column they derived from. Molnar merely said they may be fragments of ribs, while Nessov thought they probably belonged to marine reptiles. There is no evidence they belong to the same animal as the metapodial, as Kiprijanow only says they "were found all together in the Seweri Osteolith" and were fossilized identically. Unfortunately, dinosaurian rib morphology has been largely ignored by most authors so comparison is difficult. Despite this, comparison to theropod, sauropod and ornithopod dorsal ribs shows at least two of the elements differ in having the proximal broad area too proximodistally extensive compared to shaft width. In this they are more similar to theropod cervical ribs, such as those of Tyrannosaurus. Assuming they are theropod cervical ribs, they are not from abelisaurs since their shafts lack a flange. The concave and possibly crushed areas on the one specimen might suggest pneumaticity as is common in neotheropods, however the cross section shows it is solid. They are also roughly similar to sauropod cervical ribs, though in medial view sauropods have a strut extending perpendicular to the shaft from the tuberculum which is missing in schmidti. Another possibility for at least some of the elements is that they are the medial ends of of medial theropod gastralia (other dinosaurs of the time lacked gastralia), which share the slightly expanded end and transition from plate-like medial portion to rod-like lateral portion. In either case they are undiagnostic and Nessov's suggestion they belong to ichthyosaurs or plesiosaurs should be seriously considered as well, by someone more familiar with those animals than I am. Kiprijanow devotes several figures and most of his description to schmidti's histology, which could prove useful to someone knowledgable on that subject.

Nessov, 1995. Dinosaurs of nothern Eurasia: New data about assemblages, ecology, and paleobiogeography. Institute for Scientific Research on the Earth's Crust, St. Petersburg State University, St. Petersburg. 1-156.

Storrs, Arkhangelskii and Efimov, 2000. Mesozoic marine reptiles of Russia and other former Soviet republics. in Benton, Shishkin, Unwin and Kurochkin (eds.). The Age of Dinosaurs in Russia and Mongolia. Cambridge University Press. 187-210.

Holtz, Molnar and Currie, 2004. Basal Tetanurae. in Weishampel, Dodson and Osmolska (eds.). The Dinosauria Second Edition. University of California Press. 71-110.

So, do you agree with my assessment based on the figures? Who knew it was a sauropod?! It's only my second post and I'm barging in on SV-POW's territory. What's next for the blog? Probably not another obscure Soviet 'megalosaur' described before WWII. I might branch out to some other part of Asia at least. As before, write me at Mickey_Mortimer111@msn.com for a copy of the description in all its German histological glory.